I suppose that you can't update from v1 to v2 through Update FileSystem function of HDToolBox?
You can, but SFS2 will consider the SFS1 filesystem corrupt. So no, you can't, really...
SFS1 and SFS2 are incompatible, and you can't switch between. You need to backup, install the fs, quickformat, restore files.
Also, the word is that SFS2 is a bit experimental for now, and as such it's should not yet be trusted your invaluable data. Finally: OS 3.x has no support for large files, so you're probably not able to use >4GB files anyway.